tests/testthat/test_digestFastqs_primers.R
In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data
test_that("digestFastqs works as expected for primer experiments", {
fqt1 <- system.file("extdata/leujunt0_1.fastq.gz", package = "mutscan")
fqt2 <- system.file("extdata/leujunt0_2.fastq.gz", package = "mutscan")
leu <- c(ATF2 = "GATCCTGATGAAAAAAGGAGAAAGTTTTTAGAGCGAAATAGAGCAGCAGCTTCAAGATGCCGACAAAAAAGGAAAGTCTGGGTTCAGTCTTTAGAGAAGAAAGCTGAAGACTTGAGTTCATTAAATGGTCAGCTGCAGAGTGAAGTCACCCTGCTGAGAAATGAAGTGGCACAGCTGAAACAGCTTCTTCTGGCT",
ATF7 = "GATCCAGATGAGCGACGGCAGCGCTTTCTGGAGCGCAACCGGGCTGCAGCCTCCCGCTGCCGCCAAAAGCGAAAGCTGTGGGTGTCCTCCCTAGAGAAGAAGGCCGAAGAACTCACTTCTCAGAACATTCAGCTGAGTAATGAAGTCACATTACTACGCAATGAGGTGGCCCAGTTGAAACAGCTACTGTTAGCT",
CREB5 = "GATCCGGACGAGAGGCGGCGGAAATTTCTGGAACGGAACCGGGCAGCTGCCACCCGCTGCAGACAGAAGAGGAAGGTCTGGGTGATGTCATTGGAAAAGAAAGCAGAAGAACTCACCCAGACAAACATGCAGCTTCAGAATGAAGTGTCTATGTTGAAAAATGAGGTGGCCCAGCTGAAACAGTTGTTGTTAACA",
ATF3 = "GAAGAAGATGAAAGGAAAAAGAGGCGACGAGAAAGAAATAAGATTGCAGCTGCAAAGTGCCGAAACAAGAAGAAGGAGAAGACGGAGTGCCTGCAGAAAGAGTCGGAGAAGCTGGAAAGTGTGAATGCTGAACTGAAGGCTCAGATTGAGGAGCTCAAGAACGAGAAGCAGCATTTGATATACATGCTCAACCTT",
JDP2 = "GAGGAAGAGGAGCGAAGGAAAAGGCGCCGGGAGAAGAACAAAGTCGCAGCAGCCCGATGCCGGAACAAGAAGAAGGAGCGCACGGAGTTTCTGCAGCGGGAATCCGAGCGGCTGGAACTCATGAACGCAGAGCTGAAGACCCAGATTGAGGAGCTGAAGCAGGAGCGGCAGCAGCTCATCCTGATGCTGAACCGA",
ATF4 = "GAGAAACTGGATAAGAAGCTGAAAAAAATGGAGCAAAACAAGACAGCAGCCACTAGGTACCGCCAGAAGAAGAGGGCGGAGCAGGAGGCTCTTACTGGTGAGTGCAAAGAGCTGGAAAAGAAGAACGAGGCTCTAAAAGAGAGGGCGGATTCCCTGGCCAAGGAGATCCAGTACCTGAAAGATTTGATAGAAGAG",
ATF5 = "ACCCGAGGGGACCGCAAGCAAAAGAAGAGAGACCAGAACAAGTCGGCGGCTCTGAGGTACCGCCAGCGGAAGCGGGCAGAGGGTGAGGCCCTGGAGGGCGAGTGCCAGGGGCTGGAGGCACGGAATCGCGAGCTGAAGGAACGGGCAGAGTCCGTGGAGCGCGAGATCCAGTACGTCAAGGACCTGCTCATCGAG",
CREBZF = "AGTCCCCGGAAGGCGGCGGCGGCCGCTGCCCGCCTTAATCGACTGAAGAAGAAGGAGTACGTGATGGGGCTGGAGAGTCGAGTCCGGGGTCTGGCAGCCGAGAACCAGGAGCTGCGGGCCGAGAATCGGGAGCTGGGCAAACGCGTACAGGCACTGCAGGAGGAGAGTCGCTACCTACGGGCAGTCTTAGCCAAC",
BATF2 = "CCCAAGGAGCAACAAAGGCAGCTGAAGAAGCAGAAGAACCGGGCAGCCGCCCAGCGAAGCCGGCAGAAGCACACAGACAAGGCAGACGCCCTGCACCAGCAGCACGAGTCTCTGGAAAAAGACAACCTCGCCCTGCGGAAGGAGATCCAGTCCCTGCAGGCCGAGCTGGCGTGGTGGAGCCGGACCCTGCACGTG",
BATF3 = "GAGGATGATGACAGGAAGGTCCGAAGGAGAGAAAAAAACCGAGTTGCTGCTCAGAGAAGTCGGAAGAAGCAGACCCAGAAGGCTGACAAGCTCCATGAGGAATATGAGAGCCTGGAGCAAGAAAACACCATGCTGCGGAGAGAGATCGGGAAGCTGACAGAGGAGCTGAAGCACCTGACAGAGGCACTGAAGGAG",
CEBPE = "AAAGATAGCCTTGAGTACCGGCTGAGGCGGGAGCGCAACAACATCGCCGTGCGCAAGAGCCGAGACAAGGCCAAGAGGCGCATTCTGGAGACGCAGCAGAAGGTGCTGGAGTACATGGCAGAGAACGAGCGCCTCCGCAGCCGCGTGGAGCAGCTCACCCAGGAGCTAGACACCCTCCGCAACCTCTTCCGCCAG",
BACH1 = "CTGGATTGTATCCATGATATTCGAAGAAGAAGTAAAAACAGAATTGCTGCACAGCGCTGTCGCAAGAGAAAACTTGACTGTATACAGAATCTTGAATCAGAAATTGAGAAGCTGCAAAGTGAAAAGGAGAGCTTGTTGAAGGAAAGAGATCACATTTTGTCAACTCTGGGTGAGACAAAGCAGAACCTAACTGGA",
BACH2 = "TTAGAGTTTATTCATGATGTCCGACGGCGCAGCAAGAACCGCATCGCGGCCCAGCGCTGCCGCAAAAGGAAACTGGACTGTATTCAGAATTTAGAATGTGAAATCCGCAAATTGGTGTGTGAGAAAGAGAAACTGTTGTCAGAGAGGAATCAACTGAAAGCATGCATGGGGGAACTGTTGGACAACTTCTCCTGC",
NFE2L1 = "CTGAGCCTCATCCGAGACATCCGGCGCCGGGGCAAGAACAAGATGGCGGCGCAGAACTGCCGCAAGCGCAAGCTGGACACCATCCTGAATCTGGAGCGTGATGTGGAGGACCTGCAGCGTGACAAAGCCCGGCTGCTGCGGGAGAAAGTGGAGTTCCTGCGCTCCCTGCGACAGATGAAGCAGAAGGTCCAGAGC",
NFE2 = "CTAGCGCTAGTCCGGGACATCCGACGACGGGGCAAAAACAAGGTGGCAGCCCAGAACTGCCGCAAGAGGAAGCTGGAAACCATTGTGCAGCTGGAGCGGGAGCTGGAGCGGCTGACCAATGAACGGGAGCGGCTTCTCAGGGCCCGCGGGGAGGCAGACCGGACCCTGGAGGTCATGCGCCAACAGCTGACAGAG",
NFIL3 = "AAGAAAGATGCTATGTATTGGGAAAAAAGGCGGAAAAATAATGAAGCTGCCAAAAGATCTCGTGAGAAGCGTCGACTGAATGACCTGGTTTTAGAGAACAAACTAATTGCACTGGGAGAAGAAAACGCCACTTTAAAAGCTGAGCTGCTTTCACTAAAATTAAAGTTTGGTTTAATTAGCTCCACAGCATATGCT",
FOS = "GAAGAAGAAGAGAAAAGGAGAATCCGAAGGGAAAGGAATAAGATGGCTGCAGCCAAATGCCGCAACCGGAGGAGGGAGCTGACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTAGAGTTCATCCTGGCAGCT",
FOSB = "GAGGAAGAGGAGAAGCGAAGGGTGCGCCGGGAACGAAATAAACTAGCAGCAGCTAAATGCAGGAACCGGCGGAGGGAGCTGACCGACCGACTCCAGGCGGAGACAGATCAGTTGGAGGAAGAAAAAGCAGAGCTGGAGTCGGAGATCGCCGAGCTCCAAAAGGAGAAGGAACGTCTGGAGTTTGTGCTGGTGGCC",
FOSL1 = "GAGGAAGAGGAGCGCCGCCGAGTAAGGCGCGAGCGGAACAAGCTGGCTGCGGCCAAGTGCAGGAACCGGAGGAAGGAACTGACCGACTTCCTGCAGGCGGAGACTGACAAACTGGAAGATGAGAAATCTGGGCTGCAGCGAGAGATTGAGGAGCTGCAGAAGCAGAAGGAGCGCCTAGAGCTGGTGCTGGAAGCC",
FOSL2 = "GAAGAGGAGGAGAAGCGTCGCATCCGGCGGGAGAGGAACAAGCTGGCTGCAGCCAAGTGCCGGAACCGACGCCGGGAGCTGACAGAGAAGCTGCAGGCGGAGACAGAGGAGCTGGAGGAGGAGAAGTCAGGCCTGCAGAAGGAGATTGCTGAGCTGCAGAAGGAGAAGGAGAAGCTGGAGTTCATGTTGGTGGCT",
MAFB = "GTGATCCGCCTGAAGCAGAAGCGGCGGACCCTGAAGAACCGGGGCTACGCCCAGTCTTGCAGGTATAAACGCGTCCAGCAGAAGCACCACCTGGAGAATGAGAAGACGCAGCTCATTCAGCAGGTGGAGCAGCTTAAGCAGGAGGTGTCCCGGCTGGCCCGCGAGAGAGACGCCTACAAGGTCAAGTGCGAGAAA",
JUN = "CAGGAGCGGATCAAGGCGGAGAGGAAGCGCATGAGGAACCGCATCGCTGCCTCCAAGTGCCGAAAAAGGAAGCTGGAGAGAATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTTAAACAGAAAGTCATGAAC",
JUNB = "CAAGAGCGCATCAAAGTGGAGCGCAAGCGGCTGCGGAACCGGCTGGCGGCCACCAAGTGCCGGAAGCGGAAGCTGGAGCGCATCGCGCGCCTGGAGGACAAGGTGAAGACGCTCAAGGCCGAGAACGCGGGGCTGTCGAGTACCGCCGGCCTCCTCCGGGAGCAGGTGGCCCAGCTCAAACAGAAGGTCATGACC",
JUND = "CAGGAGCGCATCAAGGCGGAGCGCAAGCGGCTGCGCAACCGCATCGCCGCCTCCAAGTGCCGCAAGCGCAAGCTGGAGCGCATCTCGCGCCTGGAAGAGAAAGTGAAGACCCTCAAGAGTCAGAACACGGAGCTGGCGTCCACGGCGAGCCTGCTGCGCGAGCAGGTGGCGCAGCTCAAGCAGAAAGTCCTCAGC",
CREB3 = "GAACAAATTCTGAAACGTGTGCGGAGGAAGATTCGAAATAAAAGATCTGCTCAAGAGAGCCGCAGGAAAAAGAAGGTGTATGTTGGGGGTTTAGAGAGCAGGGTCTTGAAATACACAGCCCAGAATATGGAGCTTCAGAACAAAGTACAGCTTCTGGAGGAACAGAATTTGTCCCTTCTAGATCAACTGAGGAAA",
HLF = "CTGAAGGATGACAAGTACTGGGCAAGGCGCAGAAAGAACAACATGGCAGCCAAGCGCTCCCGCGACGCCCGGAGGCTGAAAGAGAACCAGATCGCCATCCGGGCCTCGTTCCTGGAGAAGGAGAACTCGGCCCTCCGCCAGGAGGTGGCTGACTTGAGGAAGGAGCTGGGCAAATGCAAGAACATACTTGCCAAG",
MAFG = "ATCGTCCAGCTGAAGCAGCGCCGGCGCACGCTCAAGAACCGCGGCTACGCTGCCAGCTGCCGCGTGAAGCGGGTGACGCAGAAGGAGGAGCTGGAGAAGCAGAAGGCGGAGCTGCAGCAGGAGGTGGAGAAGCTGGCCTCAGAGAACGCCAGCATGAAGCTGGAGCTCGACGCGCTGCGCTCCAAGTACGAGGCG",
MAFK = "GTGACCCGCCTGAAGCAGCGTCGGCGCACACTCAAGAACCGCGGCTACGCGGCCAGCTGCCGCATCAAGCGGGTGACGCAGAAGGAGGAGCTGGAGCGGCAGCGCGTGGAGCTGCAGCAGGAGGTGGAGAAGCTGGCGCGTGAGAACAGCAGCATGCGGCTGGAGCTGGACGCCCTGCGCTCCAAGTACGAGGCG",
XBP1 = "AGCCCCGAGGAGAAGGCGCTGAGGAGGAAACTGAAAAACAGAGTAGCAGCTCAGACTGCCAGAGATCGAAAGAAGGCTCGAATGAGTGAGCTGGAACAGCAAGTGGTAGATTTAGAAGAAGAGAACCAAAAACTTTTGCTAGAAAATCAGCTTTTACGAGAGAAAACTCATGGCCTTGTAGTTGAGAACCAGGAG",
ATF6 = "ATTGCTGTGCTAAGGAGACAGCAACGTATGATAAAAAATCGAGAATCCGCTTGTCAGTCTCGCAAGAAGAAGAAAGAATATATGCTAGGGTTAGAGGCGAGATTAAAGGCTGCCCTCTCAGAAAACGAGCAACTGAAGAAAGAAAATGGAACACTGAAGCGGCAGCTGGATGAAGTTGTGTCAGAGAACCAGAGG",
ATF6B = "GCAAAGCTGCTGAAGCGGCAGCAGCGAATGATCAAGAACCGGGAGTCAGCCTGCCAGTCCCGGAGAAAGAAGAAAGAGTATCTGCAGGGACTGGAGGCTCGGCTGCAAGCAGTACTGGCTGACAACCAGCAGCTCCGCCGAGAGAATGCTGCCCTCCGGCGGCGGCTGGAGGCCCTGCTGGCTGAAAACAGCGAG",
CEBPA = "AAGAACAGCAACGAGTACCGGGTGCGGCGCGAGCGCAACAACATCGCGGTGCGCAAGAGCCGCGACAAGGCCAAGCAGCGCAACGTGGAGACGCAGCAGAAGGTGCTGGAGCTGACCAGTGACAATGACCGCCTGCGCAAGCGGGTGGAACAGCTGAGCCGCGAACTGGACACGCTGCGGGGCATCTTCCGCCAG",
CEBPB = "AAGCACAGCGACGAGTACAAGATCCGGCGCGAGCGCAACAACATCGCCGTGCGCAAGAGCCGCGACAAGGCCAAGATGCGCAACCTGGAGACGCAGCACAAGGTCCTGGAGCTCACGGCCGAGAACGAGCGGCTGCAGAAGAAGGTGGAGCAGCTGTCGCGCGAGCTCAGCACCCTGCGGAACTTGTTCAAGCAG",
CEBPD = "CGCGGCAGCCCCGAGTACCGGCAGCGGCGCGAGCGCAACAACATCGCCGTGCGCAAGAGCCGCGACAAGGCCAAGCGGCGCAACCAGGAGATGCAGCAGAAGTTGGTGGAGCTGTCGGCTGAGAACGAGAAGCTGCACCAGCGCGTGGAGCAGCTCACGCGGGACCTGGCCGGCCTCCGGCAGTTCTTCAAGCAG",
CEBPG = "CGAAACAGTGACGAGTATCGGCAACGCCGAGAGAGGAACAACATGGCTGTGAAAAAGAGCCGGTTGAAAAGCAAGCAGAAAGCACAAGACACACTGCAGAGAGTCAATCAGCTCAAAGAAGAGAATGAACGGTTGGAAGCAAAAATCAAATTGCTGACCAAGGAATTAAGTGTACTCAAAGATTTGTTTCTTGAG",
CREB1 = "GAAGCAGCACGAAAGAGAGAGGTCCGTCTAATGAAGAACAGGGAAGCAGCTCGAGAGTGTCGTAGAAAGAAGAAAGAATATGTGAAATGTTTAGAAAACAGAGTGGCAGTGCTTGAAAATCAAAACAAGACATTGATTGAGGAGCTAAAAGCACTTAAGGACCTTTACTGCCACAAATCAGAT",
CREB3L1 = "GAGAAGGCCTTGAAGAGAGTCCGGAGGAAAATCAAGAACAAGATCTCAGCCCAGGAGAGCCGTCGTAAGAAGAAGGAGTATGTGGAGTGTCTAGAAAAGAAGGTGGAGACATTTACATCTGAGAACAATGAACTGTGGAAGAAGGTGGAGACCCTGGAGAATGCCAACAGGACCCTGCTCCAGCAGCTGCAGAAA",
CREB3L2 = "GAGAAGGCCCTGAAGAAAATTCGGAGGAAGATCAAGAATAAGATTTCTGCTCAGGAAAGTAGGAGAAAGAAGAAAGAATACATGGACAGCCTGGAGAAAAAAGTGGAGTCTTGTTCAACTGAGAACTTGGAGCTTCGGAAGAAGGTAGAGGTTCTAGAGAACACTAATAGGACTCTCCTTCAGCAACTCCAGAAG",
CREB3L3 = "GAGCGAGTGCTGAAAAAAATCCGCCGGAAAATCCGGAACAAGCAGTCGGCGCAAGAAAGCAGGAAGAAGAAGAAGGAATATATCGATGGCCTGGAGACTCGGATGTCAGCTTGCACTGCTCAGAATCAGGAGTTACAGAGGAAAGTCTTGCATCTCGAGAAGCAAAACCTGTCCCTCTTGGAGCAACTGAAGAAA",
CREB3L4 = "GAGAGGGTCCTCAAGAAGGTCAGGAGGAAAATCCGTAACAAGCAGTCAGCTCAGGACAGTCGGCGGCGGAAGAAGGAGTACATTGATGGGCTGGAGAGCAGGGTGGCAGCCTGTTCTGCACAGAACCAAGAATTACAGAAAAAAGTCCAGGAGCTGGAGAGGCACAACATCTCCTTGGTAGCTCAGCTCCGCCAG",
CREBL2 = "CCAGCCAAAATTGACTTGAAAGCAAAACTTGAGAGGAGCCGGCAGAGTGCAAGAGAATGCCGAGCCCGAAAAAAGCTGAGATATCAGTATTTGGAAGAGTTGGTATCCAGTCGAGAAAGAGCTATATGTGCCCTCAGAGAGGAACTGGAAATGTACAAGCAGTGGTGCATGGCAATGGACCAAGGAAAAATCCCT",
CREBRF = "CCCTTAACAGCCCGACCAAGGTCAAGGAAGGAAAAAAATAAGCTGGCTTCCAGAGCTTGTCGGTTAAAGAAGAAAGCCCAGTATGAAGCTAATAAAGTGAAATTATGGGGCCTCAACACAGAATATGATAATTTATTGTTTGTAATCAACTCCATCAAGCAAGAGATTGTAAACCGGGTACAGAATCCAAGAGAT",
DBP = "CAGAAGGATGAGAAATACTGGAGCCGGCGGTACAAGAACAACGAGGCAGCCAAGCGGTCCCGTGACGCCCGGCGGCTCAAGGAGAACCAGATATCGGTGCGGGCGGCCTTCCTGGAGAAGGAGAACGCCCTGCTGCGGCAGGAAGTTGTGGCCGTGCGCCAGGAGCTGTCCCACTACCGCGCCGTGCTGTCCCGA",
NFE2L2 = "CTTGCATTAATTCGGGATATACGTAGGAGGGGTAAGAATAAAGTGGCTGCTCAGAATTGCAGAAAAAGAAAACTGGAAAATATAGTAGAACTAGAGCAAGATTTAGATCATTTGAAAGATGAAAAAGAAAAATTGCTCAAAGAAAAAGGAGAAAATGACAAAAGCCTTCACCTACTGAAAAAACAACTCAGCACC",
NFE2L3 = "GTCTCACTTATCCGTGACATCAGACGAAGAGGGAAAAATAAAGTTGCTGCGCAGAACTGTCGTAAACGCAAATTGGACATAATTTTGAATTTAGAAGATGATGTATGTAACTTGCAAGCAAAGAAGGAAACTCTTAAGAGAGAGCAAGCACAATGTAACAAAGCTATTAACATAATGAAACAGAAACTGCATGAC",
TEF = "CAGAAGGATGAAAAGTACTGGACAAGACGCAAGAAGAACAACGTGGCAGCTAAACGGTCACGGGATGCCCGGCGCCTGAAAGAGAATCAGATCACCATCCGGGCAGCCTTCCTGGAGAAGGAGAACACAGCCCTGCGGACGGAGGTGGCCGAGCTACGCAAGGAGGTGGGCAAGTGCAAGACCATCGTGTCCAAG"
)
## default arguments
Ldef <- list(
fastqForward = fqt1, fastqReverse = fqt2,
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SPV", elementsReverse = "SPVS",
elementLengthsForward = c(-1, -1, -1),
elementLengthsReverse = c(-1, -1, 96, -1),
adapterForward = "",
adapterReverse = "",
primerForward = "GTCAGGTGGAGGCGGATCC",
primerReverse = "GAAAAAGGAAGCTGGAGAGA",
wildTypeForward = leu,
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "",
constantReverse = "",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 0,
nbrMutatedCodonsMaxReverse = 1,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1000,
maxReadLength = 1024
)
res <- do.call(digestFastqs, Ldef)
expect_equal(res$filterSummary$nbrTotal, 1000L)
expect_equal(res$filterSummary$f1_nbrAdapter, 0L)
expect_equal(res$filterSummary$f2_nbrNoPrimer, 126L)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, 0L)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, 0L)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, 0L)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, 76L)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, 0L)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, 0L)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, 0L)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, 58L + 137L)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, 0L)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, 3L)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, 0L)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, 0L)
expect_equal(res$filterSummary$nbrRetained, 600L)
for (nm in setdiff(names(Ldef), c("forbiddenMutatedCodonsForward", "forbiddenMutatedCodonsReverse", "verbose", "fastqForward", "fastqReverse"))) {
expect_equal(res$parameters[[nm]], Ldef[[nm]], ignore_attr = TRUE)
}
for (nm in c("fastqForward", "fastqReverse")) {
expect_equal(res$parameters[[nm]], normalizePath(Ldef[[nm]], mustWork = FALSE),
ignore_attr = TRUE)
}
expect_equal(sum(res$summaryTable$nbrReads), res$filterSummary$nbrRetained)
expect_equal(sum(res$summaryTable$nbrReads == 2), 11L)
expect_equal(sort(res$summaryTable$mutantName[res$summaryTable$nbrReads == 2]),
sort(c("BACH2.0.WT_r.6.CCC", "BATF2.0.WT_r.21.TGG", "BATF2.0.WT_r.7.GGG", "CEBPB.0.WT_r.12.CTC",
"CEBPD.0.WT_r.13.CCC", "CEBPD.0.WT_r.23.GAG", "CREB3L3.0.WT_r.22.GGG",
"FOSL1.0.WT_r.22.CCC", "FOSL2.0.WT_r.13.GGG", "JUNB.0.WT_r.0.WT", "XBP1.0.WT_r.0.WT")))
expect_equal(sort(res$summaryTable$mutantNameCodon[res$summaryTable$nbrReads == 2]),
sort(c("BACH2.0.WT_r.6.CCC", "BATF2.0.WT_r.21.TGG", "BATF2.0.WT_r.7.GGG", "CEBPB.0.WT_r.12.CTC",
"CEBPD.0.WT_r.13.CCC", "CEBPD.0.WT_r.23.GAG", "CREB3L3.0.WT_r.22.GGG",
"FOSL1.0.WT_r.22.CCC", "FOSL2.0.WT_r.13.GGG", "JUNB.0.WT_r.0.WT", "XBP1.0.WT_r.0.WT")))
expect_equal(sort(res$summaryTable$mutantNameBase[res$summaryTable$nbrReads == 2]),
sort(c("BACH2.0.WT_r.16.C_r.17.C_r.18.C", "BATF2.0.WT_r.61.T_r.62.G",
"BATF2.0.WT_r.19.G_r.20.G_r.21.G", "CEBPB.0.WT_r.34.C_r.35.T_r.36.C",
"CEBPD.0.WT_r.37.C_r.39.C", "CEBPD.0.WT_r.67.G_r.69.G",
"CREB3L3.0.WT_r.65.G_r.66.G", "FOSL1.0.WT_r.64.C",
"FOSL2.0.WT_r.38.G_r.39.G", "JUNB.0.WT_r.0.WT", "XBP1.0.WT_r.0.WT")))
expect_equal(sort(res$summaryTable$mutantNameBaseHGVS[res$summaryTable$nbrReads == 2]),
sort(c("BACH2:c_r:c.16_18delinsCCC", "BATF2:c_r:c.61_62delinsTG",
"BATF2:c_r:c.19_21delinsGGG", "CEBPB:c_r:c.34_36delinsCTC",
"CEBPD:c_r:c.37_39delinsCCC", "CEBPD:c_r:c.67_69delinsGAG",
"CREB3L3:c_r:c.65_66delinsGG", "FOSL1:c_r:c.64G>C",
"FOSL2:c_r:c.38_39delinsGG", "JUNB:c_r:c", "XBP1:c_r:c")))
expect_equal(sort(res$summaryTable$mutantNameAAHGVS[res$summaryTable$nbrReads == 2]),
sort(c("BACH2:p_r:p.(Glu6Pro)", "BATF2:p_r:p.(Thr21Trp)",
"BATF2:p_r:p.(Lys7Gly)", "CEBPB:p_r:p.(Lys12Leu)",
"CEBPD:p_r:p.(Ala13Pro)", "CEBPD:p_r:p.(Asn23Glu)",
"CREB3L3:p_r:p.(Ala22Gly)", "FOSL1:p_r:p.(Ala22Pro)",
"FOSL2:p_r:p.(Ala13Gly)", "JUNB:p_r:p", "XBP1:p_r:p")))
expect_equal(res$summaryTable$nbrUmis, rep(0L, nrow(res$summaryTable))) ## no UMIs in this experiment
## ---------------------------------------------------------------------------
## Test that we get the same results with useTreeWTmatch = TRUE
## ---------------------------------------------------------------------------
Ldef$useTreeWTmatch <- TRUE
res2 <- do.call(digestFastqs, Ldef)
expect_equal(res$filterSummary$nbrTotal, res2$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res2$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res2$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res2$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res2$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res2$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res2$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res2$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res2$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res2$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res2$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res2$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res2$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res2$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res2$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res2$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res2$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res2$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res2$summaryTable$sequence)
## ---------------------------------------------------------------------------
## Test aggregating across groups of wildtype sequences
## ---------------------------------------------------------------------------
Ldef <- list(
fastqForward = fqt1, fastqReverse = fqt2,
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SPV", elementsReverse = "SPSS",
elementLengthsForward = c(-1, -1, -1),
elementLengthsReverse = c(-1, -1, 96, -1),
adapterForward = "",
adapterReverse = "",
primerForward = "GTCAGGTGGAGGCGGATCC",
primerReverse = "GAAAAAGGAAGCTGGAGAGA",
wildTypeForward = leu,
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "",
constantReverse = "",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 0,
nbrMutatedCodonsMaxReverse = 0,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1000,
maxReadLength = 1024
)
res1 <- do.call(digestFastqs, Ldef)
leu2 <- leu
names(leu2)[1:5] <- "ATF2"
Ldef$wildTypeForward <- leu2
res2 <- do.call(digestFastqs, Ldef)
expect_identical(res1$filterSummary, res2$filterSummary)
expect_identical(res1$errorStatistics, res2$errorStatistics)
expect_equal(nrow(res1$summaryTable), nrow(res2$summaryTable) + 4)
idx <- which(!res1$summaryTable$mutantName %in% paste0(names(leu)[1:5], ".0.WT_r.0.WT"))
expect_identical(res1$summaryTable[idx, ],
res2$summaryTable[match(res1$summaryTable$mutantName[idx],
res2$summaryTable$mutantName), ],
ignore_attr = TRUE)
expect_equal(sum(res1$summaryTable[-idx, "nbrReads"]),
res2$summaryTable[res2$summaryTable$mutantName ==
paste0(names(leu2)[1], ".0.WT_r.0.WT"), "nbrReads"])
})
fmicompbio/mutscan documentation built on Oct. 24, 2024, 2:41 p.m.
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test_that("digestFastqs works as expected for primer experiments", {
fqt1 <- system.file("extdata/leujunt0_1.fastq.gz", package = "mutscan")
fqt2 <- system.file("extdata/leujunt0_2.fastq.gz", package = "mutscan")
leu <- c(ATF2 = "GATCCTGATGAAAAAAGGAGAAAGTTTTTAGAGCGAAATAGAGCAGCAGCTTCAAGATGCCGACAAAAAAGGAAAGTCTGGGTTCAGTCTTTAGAGAAGAAAGCTGAAGACTTGAGTTCATTAAATGGTCAGCTGCAGAGTGAAGTCACCCTGCTGAGAAATGAAGTGGCACAGCTGAAACAGCTTCTTCTGGCT",
ATF7 = "GATCCAGATGAGCGACGGCAGCGCTTTCTGGAGCGCAACCGGGCTGCAGCCTCCCGCTGCCGCCAAAAGCGAAAGCTGTGGGTGTCCTCCCTAGAGAAGAAGGCCGAAGAACTCACTTCTCAGAACATTCAGCTGAGTAATGAAGTCACATTACTACGCAATGAGGTGGCCCAGTTGAAACAGCTACTGTTAGCT",
CREB5 = "GATCCGGACGAGAGGCGGCGGAAATTTCTGGAACGGAACCGGGCAGCTGCCACCCGCTGCAGACAGAAGAGGAAGGTCTGGGTGATGTCATTGGAAAAGAAAGCAGAAGAACTCACCCAGACAAACATGCAGCTTCAGAATGAAGTGTCTATGTTGAAAAATGAGGTGGCCCAGCTGAAACAGTTGTTGTTAACA",
ATF3 = "GAAGAAGATGAAAGGAAAAAGAGGCGACGAGAAAGAAATAAGATTGCAGCTGCAAAGTGCCGAAACAAGAAGAAGGAGAAGACGGAGTGCCTGCAGAAAGAGTCGGAGAAGCTGGAAAGTGTGAATGCTGAACTGAAGGCTCAGATTGAGGAGCTCAAGAACGAGAAGCAGCATTTGATATACATGCTCAACCTT",
JDP2 = "GAGGAAGAGGAGCGAAGGAAAAGGCGCCGGGAGAAGAACAAAGTCGCAGCAGCCCGATGCCGGAACAAGAAGAAGGAGCGCACGGAGTTTCTGCAGCGGGAATCCGAGCGGCTGGAACTCATGAACGCAGAGCTGAAGACCCAGATTGAGGAGCTGAAGCAGGAGCGGCAGCAGCTCATCCTGATGCTGAACCGA",
ATF4 = "GAGAAACTGGATAAGAAGCTGAAAAAAATGGAGCAAAACAAGACAGCAGCCACTAGGTACCGCCAGAAGAAGAGGGCGGAGCAGGAGGCTCTTACTGGTGAGTGCAAAGAGCTGGAAAAGAAGAACGAGGCTCTAAAAGAGAGGGCGGATTCCCTGGCCAAGGAGATCCAGTACCTGAAAGATTTGATAGAAGAG",
ATF5 = "ACCCGAGGGGACCGCAAGCAAAAGAAGAGAGACCAGAACAAGTCGGCGGCTCTGAGGTACCGCCAGCGGAAGCGGGCAGAGGGTGAGGCCCTGGAGGGCGAGTGCCAGGGGCTGGAGGCACGGAATCGCGAGCTGAAGGAACGGGCAGAGTCCGTGGAGCGCGAGATCCAGTACGTCAAGGACCTGCTCATCGAG",
CREBZF = "AGTCCCCGGAAGGCGGCGGCGGCCGCTGCCCGCCTTAATCGACTGAAGAAGAAGGAGTACGTGATGGGGCTGGAGAGTCGAGTCCGGGGTCTGGCAGCCGAGAACCAGGAGCTGCGGGCCGAGAATCGGGAGCTGGGCAAACGCGTACAGGCACTGCAGGAGGAGAGTCGCTACCTACGGGCAGTCTTAGCCAAC",
BATF2 = "CCCAAGGAGCAACAAAGGCAGCTGAAGAAGCAGAAGAACCGGGCAGCCGCCCAGCGAAGCCGGCAGAAGCACACAGACAAGGCAGACGCCCTGCACCAGCAGCACGAGTCTCTGGAAAAAGACAACCTCGCCCTGCGGAAGGAGATCCAGTCCCTGCAGGCCGAGCTGGCGTGGTGGAGCCGGACCCTGCACGTG",
BATF3 = "GAGGATGATGACAGGAAGGTCCGAAGGAGAGAAAAAAACCGAGTTGCTGCTCAGAGAAGTCGGAAGAAGCAGACCCAGAAGGCTGACAAGCTCCATGAGGAATATGAGAGCCTGGAGCAAGAAAACACCATGCTGCGGAGAGAGATCGGGAAGCTGACAGAGGAGCTGAAGCACCTGACAGAGGCACTGAAGGAG",
CEBPE = "AAAGATAGCCTTGAGTACCGGCTGAGGCGGGAGCGCAACAACATCGCCGTGCGCAAGAGCCGAGACAAGGCCAAGAGGCGCATTCTGGAGACGCAGCAGAAGGTGCTGGAGTACATGGCAGAGAACGAGCGCCTCCGCAGCCGCGTGGAGCAGCTCACCCAGGAGCTAGACACCCTCCGCAACCTCTTCCGCCAG",
BACH1 = "CTGGATTGTATCCATGATATTCGAAGAAGAAGTAAAAACAGAATTGCTGCACAGCGCTGTCGCAAGAGAAAACTTGACTGTATACAGAATCTTGAATCAGAAATTGAGAAGCTGCAAAGTGAAAAGGAGAGCTTGTTGAAGGAAAGAGATCACATTTTGTCAACTCTGGGTGAGACAAAGCAGAACCTAACTGGA",
BACH2 = "TTAGAGTTTATTCATGATGTCCGACGGCGCAGCAAGAACCGCATCGCGGCCCAGCGCTGCCGCAAAAGGAAACTGGACTGTATTCAGAATTTAGAATGTGAAATCCGCAAATTGGTGTGTGAGAAAGAGAAACTGTTGTCAGAGAGGAATCAACTGAAAGCATGCATGGGGGAACTGTTGGACAACTTCTCCTGC",
NFE2L1 = "CTGAGCCTCATCCGAGACATCCGGCGCCGGGGCAAGAACAAGATGGCGGCGCAGAACTGCCGCAAGCGCAAGCTGGACACCATCCTGAATCTGGAGCGTGATGTGGAGGACCTGCAGCGTGACAAAGCCCGGCTGCTGCGGGAGAAAGTGGAGTTCCTGCGCTCCCTGCGACAGATGAAGCAGAAGGTCCAGAGC",
NFE2 = "CTAGCGCTAGTCCGGGACATCCGACGACGGGGCAAAAACAAGGTGGCAGCCCAGAACTGCCGCAAGAGGAAGCTGGAAACCATTGTGCAGCTGGAGCGGGAGCTGGAGCGGCTGACCAATGAACGGGAGCGGCTTCTCAGGGCCCGCGGGGAGGCAGACCGGACCCTGGAGGTCATGCGCCAACAGCTGACAGAG",
NFIL3 = "AAGAAAGATGCTATGTATTGGGAAAAAAGGCGGAAAAATAATGAAGCTGCCAAAAGATCTCGTGAGAAGCGTCGACTGAATGACCTGGTTTTAGAGAACAAACTAATTGCACTGGGAGAAGAAAACGCCACTTTAAAAGCTGAGCTGCTTTCACTAAAATTAAAGTTTGGTTTAATTAGCTCCACAGCATATGCT",
FOS = "GAAGAAGAAGAGAAAAGGAGAATCCGAAGGGAAAGGAATAAGATGGCTGCAGCCAAATGCCGCAACCGGAGGAGGGAGCTGACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTAGAGTTCATCCTGGCAGCT",
FOSB = "GAGGAAGAGGAGAAGCGAAGGGTGCGCCGGGAACGAAATAAACTAGCAGCAGCTAAATGCAGGAACCGGCGGAGGGAGCTGACCGACCGACTCCAGGCGGAGACAGATCAGTTGGAGGAAGAAAAAGCAGAGCTGGAGTCGGAGATCGCCGAGCTCCAAAAGGAGAAGGAACGTCTGGAGTTTGTGCTGGTGGCC",
FOSL1 = "GAGGAAGAGGAGCGCCGCCGAGTAAGGCGCGAGCGGAACAAGCTGGCTGCGGCCAAGTGCAGGAACCGGAGGAAGGAACTGACCGACTTCCTGCAGGCGGAGACTGACAAACTGGAAGATGAGAAATCTGGGCTGCAGCGAGAGATTGAGGAGCTGCAGAAGCAGAAGGAGCGCCTAGAGCTGGTGCTGGAAGCC",
FOSL2 = "GAAGAGGAGGAGAAGCGTCGCATCCGGCGGGAGAGGAACAAGCTGGCTGCAGCCAAGTGCCGGAACCGACGCCGGGAGCTGACAGAGAAGCTGCAGGCGGAGACAGAGGAGCTGGAGGAGGAGAAGTCAGGCCTGCAGAAGGAGATTGCTGAGCTGCAGAAGGAGAAGGAGAAGCTGGAGTTCATGTTGGTGGCT",
MAFB = "GTGATCCGCCTGAAGCAGAAGCGGCGGACCCTGAAGAACCGGGGCTACGCCCAGTCTTGCAGGTATAAACGCGTCCAGCAGAAGCACCACCTGGAGAATGAGAAGACGCAGCTCATTCAGCAGGTGGAGCAGCTTAAGCAGGAGGTGTCCCGGCTGGCCCGCGAGAGAGACGCCTACAAGGTCAAGTGCGAGAAA",
JUN = "CAGGAGCGGATCAAGGCGGAGAGGAAGCGCATGAGGAACCGCATCGCTGCCTCCAAGTGCCGAAAAAGGAAGCTGGAGAGAATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTTAAACAGAAAGTCATGAAC",
JUNB = "CAAGAGCGCATCAAAGTGGAGCGCAAGCGGCTGCGGAACCGGCTGGCGGCCACCAAGTGCCGGAAGCGGAAGCTGGAGCGCATCGCGCGCCTGGAGGACAAGGTGAAGACGCTCAAGGCCGAGAACGCGGGGCTGTCGAGTACCGCCGGCCTCCTCCGGGAGCAGGTGGCCCAGCTCAAACAGAAGGTCATGACC",
JUND = "CAGGAGCGCATCAAGGCGGAGCGCAAGCGGCTGCGCAACCGCATCGCCGCCTCCAAGTGCCGCAAGCGCAAGCTGGAGCGCATCTCGCGCCTGGAAGAGAAAGTGAAGACCCTCAAGAGTCAGAACACGGAGCTGGCGTCCACGGCGAGCCTGCTGCGCGAGCAGGTGGCGCAGCTCAAGCAGAAAGTCCTCAGC",
CREB3 = "GAACAAATTCTGAAACGTGTGCGGAGGAAGATTCGAAATAAAAGATCTGCTCAAGAGAGCCGCAGGAAAAAGAAGGTGTATGTTGGGGGTTTAGAGAGCAGGGTCTTGAAATACACAGCCCAGAATATGGAGCTTCAGAACAAAGTACAGCTTCTGGAGGAACAGAATTTGTCCCTTCTAGATCAACTGAGGAAA",
HLF = "CTGAAGGATGACAAGTACTGGGCAAGGCGCAGAAAGAACAACATGGCAGCCAAGCGCTCCCGCGACGCCCGGAGGCTGAAAGAGAACCAGATCGCCATCCGGGCCTCGTTCCTGGAGAAGGAGAACTCGGCCCTCCGCCAGGAGGTGGCTGACTTGAGGAAGGAGCTGGGCAAATGCAAGAACATACTTGCCAAG",
MAFG = "ATCGTCCAGCTGAAGCAGCGCCGGCGCACGCTCAAGAACCGCGGCTACGCTGCCAGCTGCCGCGTGAAGCGGGTGACGCAGAAGGAGGAGCTGGAGAAGCAGAAGGCGGAGCTGCAGCAGGAGGTGGAGAAGCTGGCCTCAGAGAACGCCAGCATGAAGCTGGAGCTCGACGCGCTGCGCTCCAAGTACGAGGCG",
MAFK = "GTGACCCGCCTGAAGCAGCGTCGGCGCACACTCAAGAACCGCGGCTACGCGGCCAGCTGCCGCATCAAGCGGGTGACGCAGAAGGAGGAGCTGGAGCGGCAGCGCGTGGAGCTGCAGCAGGAGGTGGAGAAGCTGGCGCGTGAGAACAGCAGCATGCGGCTGGAGCTGGACGCCCTGCGCTCCAAGTACGAGGCG",
XBP1 = "AGCCCCGAGGAGAAGGCGCTGAGGAGGAAACTGAAAAACAGAGTAGCAGCTCAGACTGCCAGAGATCGAAAGAAGGCTCGAATGAGTGAGCTGGAACAGCAAGTGGTAGATTTAGAAGAAGAGAACCAAAAACTTTTGCTAGAAAATCAGCTTTTACGAGAGAAAACTCATGGCCTTGTAGTTGAGAACCAGGAG",
ATF6 = "ATTGCTGTGCTAAGGAGACAGCAACGTATGATAAAAAATCGAGAATCCGCTTGTCAGTCTCGCAAGAAGAAGAAAGAATATATGCTAGGGTTAGAGGCGAGATTAAAGGCTGCCCTCTCAGAAAACGAGCAACTGAAGAAAGAAAATGGAACACTGAAGCGGCAGCTGGATGAAGTTGTGTCAGAGAACCAGAGG",
ATF6B = "GCAAAGCTGCTGAAGCGGCAGCAGCGAATGATCAAGAACCGGGAGTCAGCCTGCCAGTCCCGGAGAAAGAAGAAAGAGTATCTGCAGGGACTGGAGGCTCGGCTGCAAGCAGTACTGGCTGACAACCAGCAGCTCCGCCGAGAGAATGCTGCCCTCCGGCGGCGGCTGGAGGCCCTGCTGGCTGAAAACAGCGAG",
CEBPA = "AAGAACAGCAACGAGTACCGGGTGCGGCGCGAGCGCAACAACATCGCGGTGCGCAAGAGCCGCGACAAGGCCAAGCAGCGCAACGTGGAGACGCAGCAGAAGGTGCTGGAGCTGACCAGTGACAATGACCGCCTGCGCAAGCGGGTGGAACAGCTGAGCCGCGAACTGGACACGCTGCGGGGCATCTTCCGCCAG",
CEBPB = "AAGCACAGCGACGAGTACAAGATCCGGCGCGAGCGCAACAACATCGCCGTGCGCAAGAGCCGCGACAAGGCCAAGATGCGCAACCTGGAGACGCAGCACAAGGTCCTGGAGCTCACGGCCGAGAACGAGCGGCTGCAGAAGAAGGTGGAGCAGCTGTCGCGCGAGCTCAGCACCCTGCGGAACTTGTTCAAGCAG",
CEBPD = "CGCGGCAGCCCCGAGTACCGGCAGCGGCGCGAGCGCAACAACATCGCCGTGCGCAAGAGCCGCGACAAGGCCAAGCGGCGCAACCAGGAGATGCAGCAGAAGTTGGTGGAGCTGTCGGCTGAGAACGAGAAGCTGCACCAGCGCGTGGAGCAGCTCACGCGGGACCTGGCCGGCCTCCGGCAGTTCTTCAAGCAG",
CEBPG = "CGAAACAGTGACGAGTATCGGCAACGCCGAGAGAGGAACAACATGGCTGTGAAAAAGAGCCGGTTGAAAAGCAAGCAGAAAGCACAAGACACACTGCAGAGAGTCAATCAGCTCAAAGAAGAGAATGAACGGTTGGAAGCAAAAATCAAATTGCTGACCAAGGAATTAAGTGTACTCAAAGATTTGTTTCTTGAG",
CREB1 = "GAAGCAGCACGAAAGAGAGAGGTCCGTCTAATGAAGAACAGGGAAGCAGCTCGAGAGTGTCGTAGAAAGAAGAAAGAATATGTGAAATGTTTAGAAAACAGAGTGGCAGTGCTTGAAAATCAAAACAAGACATTGATTGAGGAGCTAAAAGCACTTAAGGACCTTTACTGCCACAAATCAGAT",
CREB3L1 = "GAGAAGGCCTTGAAGAGAGTCCGGAGGAAAATCAAGAACAAGATCTCAGCCCAGGAGAGCCGTCGTAAGAAGAAGGAGTATGTGGAGTGTCTAGAAAAGAAGGTGGAGACATTTACATCTGAGAACAATGAACTGTGGAAGAAGGTGGAGACCCTGGAGAATGCCAACAGGACCCTGCTCCAGCAGCTGCAGAAA",
CREB3L2 = "GAGAAGGCCCTGAAGAAAATTCGGAGGAAGATCAAGAATAAGATTTCTGCTCAGGAAAGTAGGAGAAAGAAGAAAGAATACATGGACAGCCTGGAGAAAAAAGTGGAGTCTTGTTCAACTGAGAACTTGGAGCTTCGGAAGAAGGTAGAGGTTCTAGAGAACACTAATAGGACTCTCCTTCAGCAACTCCAGAAG",
CREB3L3 = "GAGCGAGTGCTGAAAAAAATCCGCCGGAAAATCCGGAACAAGCAGTCGGCGCAAGAAAGCAGGAAGAAGAAGAAGGAATATATCGATGGCCTGGAGACTCGGATGTCAGCTTGCACTGCTCAGAATCAGGAGTTACAGAGGAAAGTCTTGCATCTCGAGAAGCAAAACCTGTCCCTCTTGGAGCAACTGAAGAAA",
CREB3L4 = "GAGAGGGTCCTCAAGAAGGTCAGGAGGAAAATCCGTAACAAGCAGTCAGCTCAGGACAGTCGGCGGCGGAAGAAGGAGTACATTGATGGGCTGGAGAGCAGGGTGGCAGCCTGTTCTGCACAGAACCAAGAATTACAGAAAAAAGTCCAGGAGCTGGAGAGGCACAACATCTCCTTGGTAGCTCAGCTCCGCCAG",
CREBL2 = "CCAGCCAAAATTGACTTGAAAGCAAAACTTGAGAGGAGCCGGCAGAGTGCAAGAGAATGCCGAGCCCGAAAAAAGCTGAGATATCAGTATTTGGAAGAGTTGGTATCCAGTCGAGAAAGAGCTATATGTGCCCTCAGAGAGGAACTGGAAATGTACAAGCAGTGGTGCATGGCAATGGACCAAGGAAAAATCCCT",
CREBRF = "CCCTTAACAGCCCGACCAAGGTCAAGGAAGGAAAAAAATAAGCTGGCTTCCAGAGCTTGTCGGTTAAAGAAGAAAGCCCAGTATGAAGCTAATAAAGTGAAATTATGGGGCCTCAACACAGAATATGATAATTTATTGTTTGTAATCAACTCCATCAAGCAAGAGATTGTAAACCGGGTACAGAATCCAAGAGAT",
DBP = "CAGAAGGATGAGAAATACTGGAGCCGGCGGTACAAGAACAACGAGGCAGCCAAGCGGTCCCGTGACGCCCGGCGGCTCAAGGAGAACCAGATATCGGTGCGGGCGGCCTTCCTGGAGAAGGAGAACGCCCTGCTGCGGCAGGAAGTTGTGGCCGTGCGCCAGGAGCTGTCCCACTACCGCGCCGTGCTGTCCCGA",
NFE2L2 = "CTTGCATTAATTCGGGATATACGTAGGAGGGGTAAGAATAAAGTGGCTGCTCAGAATTGCAGAAAAAGAAAACTGGAAAATATAGTAGAACTAGAGCAAGATTTAGATCATTTGAAAGATGAAAAAGAAAAATTGCTCAAAGAAAAAGGAGAAAATGACAAAAGCCTTCACCTACTGAAAAAACAACTCAGCACC",
NFE2L3 = "GTCTCACTTATCCGTGACATCAGACGAAGAGGGAAAAATAAAGTTGCTGCGCAGAACTGTCGTAAACGCAAATTGGACATAATTTTGAATTTAGAAGATGATGTATGTAACTTGCAAGCAAAGAAGGAAACTCTTAAGAGAGAGCAAGCACAATGTAACAAAGCTATTAACATAATGAAACAGAAACTGCATGAC",
TEF = "CAGAAGGATGAAAAGTACTGGACAAGACGCAAGAAGAACAACGTGGCAGCTAAACGGTCACGGGATGCCCGGCGCCTGAAAGAGAATCAGATCACCATCCGGGCAGCCTTCCTGGAGAAGGAGAACACAGCCCTGCGGACGGAGGTGGCCGAGCTACGCAAGGAGGTGGGCAAGTGCAAGACCATCGTGTCCAAG"
)
## default arguments
Ldef <- list(
fastqForward = fqt1, fastqReverse = fqt2,
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SPV", elementsReverse = "SPVS",
elementLengthsForward = c(-1, -1, -1),
elementLengthsReverse = c(-1, -1, 96, -1),
adapterForward = "",
adapterReverse = "",
primerForward = "GTCAGGTGGAGGCGGATCC",
primerReverse = "GAAAAAGGAAGCTGGAGAGA",
wildTypeForward = leu,
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "",
constantReverse = "",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 0,
nbrMutatedCodonsMaxReverse = 1,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1000,
maxReadLength = 1024
)
res <- do.call(digestFastqs, Ldef)
expect_equal(res$filterSummary$nbrTotal, 1000L)
expect_equal(res$filterSummary$f1_nbrAdapter, 0L)
expect_equal(res$filterSummary$f2_nbrNoPrimer, 126L)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, 0L)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, 0L)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, 0L)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, 76L)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, 0L)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, 0L)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, 0L)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, 58L + 137L)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, 0L)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, 3L)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, 0L)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, 0L)
expect_equal(res$filterSummary$nbrRetained, 600L)
for (nm in setdiff(names(Ldef), c("forbiddenMutatedCodonsForward", "forbiddenMutatedCodonsReverse", "verbose", "fastqForward", "fastqReverse"))) {
expect_equal(res$parameters[[nm]], Ldef[[nm]], ignore_attr = TRUE)
}
for (nm in c("fastqForward", "fastqReverse")) {
expect_equal(res$parameters[[nm]], normalizePath(Ldef[[nm]], mustWork = FALSE),
ignore_attr = TRUE)
}
expect_equal(sum(res$summaryTable$nbrReads), res$filterSummary$nbrRetained)
expect_equal(sum(res$summaryTable$nbrReads == 2), 11L)
expect_equal(sort(res$summaryTable$mutantName[res$summaryTable$nbrReads == 2]),
sort(c("BACH2.0.WT_r.6.CCC", "BATF2.0.WT_r.21.TGG", "BATF2.0.WT_r.7.GGG", "CEBPB.0.WT_r.12.CTC",
"CEBPD.0.WT_r.13.CCC", "CEBPD.0.WT_r.23.GAG", "CREB3L3.0.WT_r.22.GGG",
"FOSL1.0.WT_r.22.CCC", "FOSL2.0.WT_r.13.GGG", "JUNB.0.WT_r.0.WT", "XBP1.0.WT_r.0.WT")))
expect_equal(sort(res$summaryTable$mutantNameCodon[res$summaryTable$nbrReads == 2]),
sort(c("BACH2.0.WT_r.6.CCC", "BATF2.0.WT_r.21.TGG", "BATF2.0.WT_r.7.GGG", "CEBPB.0.WT_r.12.CTC",
"CEBPD.0.WT_r.13.CCC", "CEBPD.0.WT_r.23.GAG", "CREB3L3.0.WT_r.22.GGG",
"FOSL1.0.WT_r.22.CCC", "FOSL2.0.WT_r.13.GGG", "JUNB.0.WT_r.0.WT", "XBP1.0.WT_r.0.WT")))
expect_equal(sort(res$summaryTable$mutantNameBase[res$summaryTable$nbrReads == 2]),
sort(c("BACH2.0.WT_r.16.C_r.17.C_r.18.C", "BATF2.0.WT_r.61.T_r.62.G",
"BATF2.0.WT_r.19.G_r.20.G_r.21.G", "CEBPB.0.WT_r.34.C_r.35.T_r.36.C",
"CEBPD.0.WT_r.37.C_r.39.C", "CEBPD.0.WT_r.67.G_r.69.G",
"CREB3L3.0.WT_r.65.G_r.66.G", "FOSL1.0.WT_r.64.C",
"FOSL2.0.WT_r.38.G_r.39.G", "JUNB.0.WT_r.0.WT", "XBP1.0.WT_r.0.WT")))
expect_equal(sort(res$summaryTable$mutantNameBaseHGVS[res$summaryTable$nbrReads == 2]),
sort(c("BACH2:c_r:c.16_18delinsCCC", "BATF2:c_r:c.61_62delinsTG",
"BATF2:c_r:c.19_21delinsGGG", "CEBPB:c_r:c.34_36delinsCTC",
"CEBPD:c_r:c.37_39delinsCCC", "CEBPD:c_r:c.67_69delinsGAG",
"CREB3L3:c_r:c.65_66delinsGG", "FOSL1:c_r:c.64G>C",
"FOSL2:c_r:c.38_39delinsGG", "JUNB:c_r:c", "XBP1:c_r:c")))
expect_equal(sort(res$summaryTable$mutantNameAAHGVS[res$summaryTable$nbrReads == 2]),
sort(c("BACH2:p_r:p.(Glu6Pro)", "BATF2:p_r:p.(Thr21Trp)",
"BATF2:p_r:p.(Lys7Gly)", "CEBPB:p_r:p.(Lys12Leu)",
"CEBPD:p_r:p.(Ala13Pro)", "CEBPD:p_r:p.(Asn23Glu)",
"CREB3L3:p_r:p.(Ala22Gly)", "FOSL1:p_r:p.(Ala22Pro)",
"FOSL2:p_r:p.(Ala13Gly)", "JUNB:p_r:p", "XBP1:p_r:p")))
expect_equal(res$summaryTable$nbrUmis, rep(0L, nrow(res$summaryTable))) ## no UMIs in this experiment
## ---------------------------------------------------------------------------
## Test that we get the same results with useTreeWTmatch = TRUE
## ---------------------------------------------------------------------------
Ldef$useTreeWTmatch <- TRUE
res2 <- do.call(digestFastqs, Ldef)
expect_equal(res$filterSummary$nbrTotal, res2$filterSummary$nbrTotal)
expect_equal(res$filterSummary$f1_nbrAdapter, res2$filterSummary$f1_nbrAdapter)
expect_equal(res$filterSummary$f2_nbrNoPrimer, res2$filterSummary$f2_nbrNoPrimer)
expect_equal(res$filterSummary$f3_nbrReadWrongLength, res2$filterSummary$f3_nbrReadWrongLength)
expect_equal(res$filterSummary$f4_nbrNoValidOverlap, res2$filterSummary$f4_nbrNoValidOverlap)
expect_equal(res$filterSummary$f5_nbrAvgVarQualTooLow, res2$filterSummary$f5_nbrAvgVarQualTooLow)
expect_equal(res$filterSummary$f6_nbrTooManyNinVar, res2$filterSummary$f6_nbrTooManyNinVar)
expect_equal(res$filterSummary$f7_nbrTooManyNinUMI, res2$filterSummary$f7_nbrTooManyNinUMI)
expect_equal(res$filterSummary$f8_nbrTooManyBestWTHits, res2$filterSummary$f8_nbrTooManyBestWTHits)
expect_equal(res$filterSummary$f9_nbrMutQualTooLow, res2$filterSummary$f9_nbrMutQualTooLow)
expect_equal(res$filterSummary$f10a_nbrTooManyMutCodons, res2$filterSummary$f10a_nbrTooManyMutCodons)
expect_equal(res$filterSummary$f10b_nbrTooManyMutBases, res2$filterSummary$f10b_nbrTooManyMutBases)
expect_equal(res$filterSummary$f11_nbrForbiddenCodons, res2$filterSummary$f11_nbrForbiddenCodons)
expect_equal(res$filterSummary$f12_nbrTooManyMutConstant, res2$filterSummary$f12_nbrTooManyMutConstant)
expect_equal(res$filterSummary$f13_nbrTooManyBestConstantHits, res2$filterSummary$f13_nbrTooManyBestConstantHits)
expect_equal(res$filterSummary$nbrRetained, res2$filterSummary$nbrRetained)
expect_equal(res$summaryTable$nbrReads, res2$summaryTable$nbrReads)
expect_equal(res$summaryTable$mutantName, res2$summaryTable$mutantName)
expect_equal(res$summaryTable$sequence, res2$summaryTable$sequence)
## ---------------------------------------------------------------------------
## Test aggregating across groups of wildtype sequences
## ---------------------------------------------------------------------------
Ldef <- list(
fastqForward = fqt1, fastqReverse = fqt2,
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SPV", elementsReverse = "SPSS",
elementLengthsForward = c(-1, -1, -1),
elementLengthsReverse = c(-1, -1, 96, -1),
adapterForward = "",
adapterReverse = "",
primerForward = "GTCAGGTGGAGGCGGATCC",
primerReverse = "GAAAAAGGAAGCTGGAGAGA",
wildTypeForward = leu,
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "",
constantReverse = "",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 0,
nbrMutatedCodonsMaxReverse = 0,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
filteredReadsFastqForward = "",
filteredReadsFastqReverse = "",
maxNReads = -1, verbose = FALSE,
nThreads = 1, chunkSize = 1000,
maxReadLength = 1024
)
res1 <- do.call(digestFastqs, Ldef)
leu2 <- leu
names(leu2)[1:5] <- "ATF2"
Ldef$wildTypeForward <- leu2
res2 <- do.call(digestFastqs, Ldef)
expect_identical(res1$filterSummary, res2$filterSummary)
expect_identical(res1$errorStatistics, res2$errorStatistics)
expect_equal(nrow(res1$summaryTable), nrow(res2$summaryTable) + 4)
idx <- which(!res1$summaryTable$mutantName %in% paste0(names(leu)[1:5], ".0.WT_r.0.WT"))
expect_identical(res1$summaryTable[idx, ],
res2$summaryTable[match(res1$summaryTable$mutantName[idx],
res2$summaryTable$mutantName), ],
ignore_attr = TRUE)
expect_equal(sum(res1$summaryTable[-idx, "nbrReads"]),
res2$summaryTable[res2$summaryTable$mutantName ==
paste0(names(leu2)[1], ".0.WT_r.0.WT"), "nbrReads"])
})
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